[tdwg-content] Comments on Darwin Core Issue 205 (the proposed Organism term)

Steve Baskauf steve.baskauf at vanderbilt.edu
Wed Sep 17 23:45:01 CEST 2014

Just to let readers of the broader list know a bit of the history on 
this, the ad hoc group who hammered out the definitions could find no 
name for this class that satisfied everyone.  So we agreed to a name 
that was not adamantly opposed even if most people weren't completely 
happy about it.  I think it is more important to HAVE the term than for 
it to have a name that makes everyone happy. 

In an attempt to avoid another rehashing of the debate that is 
referenced in the proposal [1], I want to note that I believe that the 
purpose for creating this class is NOT to try to come up with a clear 
definition for "organism", but rather to create a term that can be used 
for typing things that would be referenced by the existing term 
dwc:individualID.  That term's definition says "Meant to accommodate 
resampling of the same individual or group for monitoring purposes."  So 
we don't intend to define class instances strictly as organisms, but 
rather as any kind of thing that is coherent enough that it could 
potentially be resampled and on which we could hang a taxonomic 
determination.  We thus dodge the question of whether fungi and wolf 
packs are really organisms.  If they can be resampled and assigned a 
taxonomic determination, they fall into the class.  I realize that this 
may make some people uncomfortable, but the reality is that this class 
already exists - it just doesn't have a term to use for typing it.  I 
think that discomfort is at least partly why we referenced OBI:0100026 - 
it gives people something more concrete to "connect" with .

I'm less concerned about mentioning OBI:010026 in a textual definition 
than I am making subclass declarations in the RDF.  That's where we run 
into unintended consequences with machine processing.  As Hilmar said, 
that horse is already out of the barn with definition of 
dwctype:MaterialSample - the implications of that kind of subclassing 
didn't get discussed very thoroughly in the run-up to 
dwctype:MaterialSample's addition to DwC.   But I'll note that in the 
current proposed suite of changes to the DwC classes [2], all of the 
"dwctype:" namespace terms would be deprecated in favor of "dwc:" 
namespace analogs.  The proposed definition of dwc:MaterialSample does 
NOT include this subclassing.  See the "justification" section at [3].  
So if the whole group of class term changes goes through as a package, 
we would no longer have any subclass relations asserted in the RDF of 
Darwin Core classes.  If people don't like that, they should speak up 
now and explain their reasoning, because that's how the proposal stands now.


[1] https://code.google.com/p/darwincore/issues/detail?id=205
[2] https://code.google.com/p/darwincore/issues/detail?id=204
[3] https://code.google.com/p/darwincore/issues/detail?id=213

Richard Pyle wrote:
> Hi Joel,
> As I fellow submitter and strong supporter of the Organism class for DwC, I,
> like you, have been uneasy with the cross-reference to OBI:0100026 in the
> definition.  It may be appropriate to include this in some sort of
> qualifying remarks about the class, but it doesn't seem to be appropriate to
> include the reference in the definition.  Even though it is somewhat
> softened by the phrase "in the sense" (as opposed to some sort of "same as"
> assertion), I would support the removal of the sentence "An organism in the
> sense used here is defined as OBI:0100026
> (http://purl.obolibrary.org/obo/OBI_0100026)." from the definition of
> dwc:Organism.
> I still believe that a human-friendly name is very helpful.  The barrier is
> not the standard or how it's named.  The barrier is how humans interpret and
> implement the standard.  Giving the class an opaque identifier (I would, of
> course, vote in favor of a UUID!) would probably create a barrier to
> progress through opacity that is greater than the barrier of confusion
> through mis-interpretation of an imperfect human-friendly name like
> "Organism".
> Of course, you didn't even indicate the term that we have been using for
> years, and which I prefer, which is "IndividualOrganism".  However, in the
> interest of progress, I strongly oppose re-opening the "name" can of worms.
> DwC is riddled with mis-applied names of things, and we can still manage to
> muddle our way through it (provided the definitions are clear).  For
> example, the term "Occurrence" has been used to represent "things" that
> range from actual occurrence instances (e.g., observations of organisms at a
> place and time), to individual organisms (e.g. specimens as a proxy to the
> occurrence of an organism at the time it was extracted from nature), to
> evidence (e.g. photographs of organisms), to occurrence-evidence instances
> (photographs of organism in nature).  Yet we still manage to exchange data
> (perhaps less efficiently than we could).
> Anyway, I support the removal of the OBI reference in the definition of
> "Occurrence", and I oppose re-visiting the issue of the label we apply to
> the proposed new dwc class.
> Aloha,
> Rich
>> -----Original Message-----
>> From: tdwg-content-bounces at lists.tdwg.org [mailto:tdwg-content-
>> bounces at lists.tdwg.org] On Behalf Of joel sachs
>> Sent: Wednesday, September 17, 2014 9:34 AM
>> To: tdwg-content at lists.tdwg.org
>> Subject: [tdwg-content] Comments on Darwin Core Issue 205 (the proposed
>> Organism term)
>> Everyone,
>> I'd like to comment on the proposed addition to Darwin Core of an
> "organism"
>> class (https://code.google.com/p/darwincore/issues/detail?id=205). I am
> one of
>> the submitters of this proposal, but I have some
>> reservations/suggestions/questions about both the definition and the name.
>> Taking them in turn:
>> The Definition
>> The proposed definition is:
>> "A particular organism or defined group of organisms considered to be
>> taxonomically homogeneous.  An organism in the sense used here is defined
> as
>> OBI:0100026 (http://purl.obolibrary.org/obo/OBI_0100026).  Instances of
> the
>> Organism class are intended to facilitate linking of one or more
> Identification
>> instances to one or more Occurrence instances.  Therefore, things that are
>> typically assigned scientific names (such as viruses, hybrids, and
> lichens) and
>> aggregates whose occurrences are typically recorded (such as packs,
> clones,
>> and colonies) are included in the scope of this class."
>> There are a few things to note here:
>> i. The definition of OBI:0100026 is "A material entity that is an
> individual living
>> system, such as animal, plant, bacteria or virus, that is capable of
> replicating or
>> reproducing, growth and maintenance in the right environment. An organism
>> may be unicellular or made up, like humans, of many billions of cells
> divided
>> into specialized tissues and organs." This definition is not internally
> consistent,
>> since it delineates organisms as being either unicellular or
> multi-cellular, while
>> at the same time explicitly including viruses, which are acellular.
>> ii. The reference to OBI:0100026 does not add clarity to the DwC
> definition,
>> since the DwC definition goes on to include the clarifying aspects of the
>> definition (viruses and lichens are organsims), while leaving out the
> muddying
>> aspects of the OBI definition (organisms are unicellular or
> multicellular). The
>> DwC definition also extends the the OBI defintion (to include wolf packs).
>> iii. The rdf definition of OBI:organism inherits axioms from the Basic
> Formal
>> Ontology (BFO). I've long argued that it's a mistake for TDWG to commit to
> any
>> particular upper ontology, as there is no consensus upper ontology. (Some
>> scientific communities use Dolce, some use SUMO, and many have
> deliberately
>> chosen to use none at all.) In general, I like the notion of Darwin Core
> as a
>> glossary of terms, on top of which various data models can be built. When
> we
>> import terms that carry with them an abundance of ontological commitment,
> it
>> raises the stakes for those who choose to use TDWG vocabularies. (In
> contrast,
>> when Darwin Core imported "Location"
>> from Dublin Core, it did so at no cost, since Dublin Core is not tied to
> any
>> particular upper world-view.)
>> The Name
>> There have been multiple debates about a good name for this class, and
> there
>> was never consensus. (In addition to "Organism", candidates included
>> "Individual", "OrganismalIndividual", "TaxonIndividualOrGroup",
>> "OrganismOrTaxonomicallyHomogenousGroupOfOrganisms",
>> "OccurringThing".) I agree that we're unlikely to agree on a consensus
> name,
>> but I question why we need a name at all. Although TDWG has traditionally
>> used transparent identifiers for terms, this has been by convention, and
> is not a
>> requirement. Is it time to test the "opaque identifier" waters? Are there
>> potential problems with having a mix of transparent and opaque identifiers
> in
>> our vocabularies? If not, could we call this class dwc:12345? Should we?
>> Thoughts on any of the above?
>> Many thanks,
>> Joel.
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Steven J. Baskauf, Ph.D., Senior Lecturer
Vanderbilt University Dept. of Biological Sciences

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